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MATLAB Crashes when Using Conda Environment Other than Base

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Peter Cook
Peter Cook on 6 Feb 2019
Edited: Seth Wagenman on 31 Aug 2020
I am having trouble using a custom conda environment in MATLAB. Here's the code I use to bootstrap a conda environment with a few packages I need from from the web:
% bootstrap a miniconda installation & python 35 environment
% choose a miniconda version,
% !!! avoid version 4.5.12 due to openSSL DLL hell !!!
condaUrl = '';
s = webread(condaUrl, weboptions('ContentType','text'));
v = unique(strcat('Miniconda3',regexp(s,'(?<=>Miniconda3)[^<>]*x86_64\.exe','match')));
vn = regexp(v,'(?<=3-)(\d*\.\d*\.\d*)','match');
verMask = cellfun(@isempty, vn);
v(verMask) = [];
vn(verMask) = [];
whichVer = listdlg('ListString',v,...
'PromptString','Select Miniconda Version',...
if isempty(whichVer)
% use the latest and greatest
urlString = '';
% use selected ver
urlString = strcat(condaUrl, v{whichVer});
fprintf('Downloading Miniconda3 Installer\n');
targetDir = websave('miniconda3.exe', urlString);
fprintf('Miniconda3 Download Complete\n');
fprintf('Installing Miniconda3\n');
disp('start /wait "" miniconda3.exe /InstallationType=JustMe /RegisterPython=0 /S /D=%UserProfile%\Miniconda')
!start /wait "" miniconda3.exe /InstallationType=JustMe /RegisterPython=0 /S /D=%UserProfile%\Miniconda
fprintf('Miniconda3 Installation Complete\n');
% build a custom conda environment for MATLAB
pyver = 3.5;
myenv = sprintf('myenv%0.0f', pyver*10);
condaCmdPath = fullfile(getenv('USERPROFILE'),'Miniconda\Scripts\activate.bat');
minicondaRoot = fullfile(getenv('USERPROFILE'),'Miniconda');
myenvRoot = fullfile(minicondaRoot, 'envs', myenv);
matlabPythonRoot = fullfile(matlabroot, 'extern', 'engines', 'python');
% write a bat file to run in condaprompt
fptr = fopen('condaSetup.bat','w');
fprintf(fptr, 'CALL %c%s%c %c%s%c\r\n', 34, condaCmdPath, 34, 34, minicondaRoot, 34);
% fprintf(fptr, '%ccomspec%c /k %c%c%s%c %c%s%c%c\r\n', 37, 37, 34, 34, condaCmdPath, 34, 34, minicondaRoot, 34, 34);
fprintf(fptr, 'CALL conda config --add channels conda-forge\r\n');
fprintf(fptr, 'CALL conda config --set proxy_servers.http http://np1prxy801:80\r\n');
fprintf(fptr, 'CALL conda config --set proxy_servers.https https://np1prxy801:80\r\n');
fprintf(fptr, 'CALL conda create -v -y -n %s python=%0.1f numpy scipy scikit-learn sklearn-contrib-py-earth\r\n', myenv, pyver);
fprintf(fptr, 'CALL conda activate %s\r\n', myenv);
fprintf(fptr, 'cd %s\r\n', matlabPythonRoot);
fprintf(fptr, 'python build -b %s install\r\n', myenvRoot);
% run "makefile"
% delete the bat file
delete 'condaSetup.bat'
% add this python environment to startup.m by appending these two lines:
% !%comspec% /c ""C:\Users\HB69954\Miniconda\Scripts\activate.bat" "C:\Users\HB69954\Miniconda\envs\myenv35""
% pyversion c:\users\hb69954\miniconda\envs\myenv35\python.exe
w = which('startup.m');
fptr = fopen(w,'r');
s = fread(fptr, inf, 'uint8=>char')';
activatePyString = '!%comspec% /c ""C:\Users\HB69954\Miniconda\Scripts\activate.bat" "C:\Users\HB69954\Miniconda\envs\myenv35""';
swapPyVersionString = 'pyversion c:\users\hb69954\miniconda\envs\myenv35\python.exe';
fptr = fopen(w,'w');
fprintf(fptr,'%s\r\n%s\r\n%s\r\n', s, activatePyString, swapPyVersionString);
This script downloads Miniconda3, installs it, and creates a conda virtual environment called myenv35.
By default, MATLAB chooses my base environment as the python version:
>> pyversion
version: '3.7'
executable: 'C:\Users\HB69954\Miniconda\python.exe'
library: 'C:\Users\HB69954\Miniconda\python37.dll'
home: 'C:\Users\HB69954\Miniconda'
isloaded: 1
I added these two lines to startup.m to load this python environment instead of the base environment:
!%comspec% /c ""C:\Users\HB69954\Miniconda\Scripts\activate.bat" "C:\Users\HB69954\Miniconda\envs\myenv35""
pyversion c:\users\hb69954\miniconda\envs\myenv35\python.exe
This apparently loads in MATLAB,
>> pyversion
version: '3.5'
executable: 'c:\users\hb69954\miniconda\envs\myenv35\python.exe'
library: 'c:\users\hb69954\miniconda\envs\myenv35\python35.dll'
home: 'c:\users\hb69954\miniconda\envs\myenv35'
isloaded: 0
I can use python standard library functions in this environment, i.e.
>> myList = py.list([1,2,3,0,8,9,7])
myList =
Python list with no properties.
[1.0, 2.0, 3.0, 0.0, 8.0, 9.0, 7.0]
>> myList.sort()
>> myList
myList =
Python list with no properties.
[0.0, 1.0, 2.0, 3.0, 7.0, 8.0, 9.0]
But MATLAB crashes whenever I try to use a library that installed in the virtual environment (i.e. numpy), MATLAB closes without issuing an error or warning.
x = py.numpy.array([1,2,3])
taskmgr doesn't show matlab.exe running in the background, and no crash dump files are created in %USERPROFILE%\AppData\Local\Temp, leading me to believe its not a real crash as much as some file/function is issuing an exit/close command to matlab.exe.
  1. Are python/conda environments supported in MATLAB? I can't think of a reason why they wouldn't be, but I haven't seen any official support documentation for them either.
  2. Could this be related to me installing MATLAB Engine for Python in the same virtual environment?
  3. Is there any other reason why swapping the python environment could be causing MATLAB to crash while running environment packages?


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Answers (2)

Julian Hapke
Julian Hapke on 19 Mar 2019
Try this:
load your environment in a seperate promt, have a look at the path variable (assuming windows here)
echo %PATH%
unload the environment (back to base), look at the %PATH% again and find out the differences. There should be some paths from the custom evironment added to the path variable.
Add those path inside matlab, for example with:
pyExec = 'C:\software\miniconda3\envs\mlpy\python.exe';
pyRoot = fileparts(pyExec);
p = getenv('PATH');
p = strsplit(p, ';');
addToPath = {
fullfile(pyRoot, 'Library', 'mingw-w64', 'bin')
fullfile(pyRoot, 'Library', 'usr', 'bin')
fullfile(pyRoot, 'Library', 'bin')
fullfile(pyRoot, 'Scripts')
fullfile(pyRoot, 'bin')
p = [addToPath(:); p(:)];
p = unique(p, 'stable');
p = strjoin(p, ';');
setenv('PATH', p);
after that MATLAB should be able to use packages from that conda environment.


Show 1 older comment
Julian Hapke
Julian Hapke on 9 Apr 2019
Adding to %PATH% with setenv should only modify the PATH in the current MATLAB Session. Outside of MATLAB everything should remain default, so I don't see a problem there.
Fahad Raza
Fahad Raza on 16 Feb 2020
@Julian Thank you. It worked absolutely fine and you saved my day.
Seth Wagenman
Seth Wagenman on 24 Aug 2020
The only way to make sure this works is to run a Python script importing a library/module not in the base conda environment. But it definitely works!

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Seth Wagenman
Seth Wagenman on 28 Aug 2020
Edited: Seth Wagenman on 31 Aug 2020
For a conda environment named "useFromMATLAB", the following code works in Windows 10/Anaconda 3. Note that if you are debugging Python at the same time, and making changes to "some_awesome_python_module," you have to reload it every time (code below starting with clear classes is how to do that).
py_root_useFromMATLAB = fileparts(C:\anaconda_3\envs\useFromMATLAB\_conda.exe);
ENV = getenv('PATH');
ENV = strsplit(ENV, ';');
items_to_add_to_path = {
fullfile(py_root_useFromMATLAB, 'Library', 'mingw-w64', 'bin')
fullfile(py_root_useFromMATLAB, 'Library', 'usr', 'bin')
fullfile(py_root_useFromMATLAB, 'Library', 'bin')
fullfile(py_root_useFromMATLAB, 'Scripts')
ENV = [items_to_add_to_path(:); ENV(:)];
ENV = unique(ENV, 'stable');
ENV = strjoin(ENV, ';');
setenv('PATH', ENV);
clear classes
module_to_load = 'some_awesome_python_module';
python_module_to_use = py.importlib.import_module(module_to_load);
% Now you can use it like output = py.some_awesome_python_module.some_awesome_python_function(input)

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Seth Wagenman
Seth Wagenman on 28 Aug 2020

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